Contacts of the strand formed by residues 127 - 137 (chain C) in PDB entry 4BEI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 127 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C PRO* 4.2 5.8 - - - -
125C ALA 3.7 1.4 + - - -
126C ASP* 1.3 74.6 - - - +
128C LYS* 1.3 61.7 + - - -
129C TYR* 3.5 7.4 - - - -
150C VAL* 3.4 2.9 - - - -
151C LYS* 2.8 34.0 + - - +
153C VAL* 4.3 18.3 - - - +
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LYS 4.4 0.2 - - - +
82C GLY* 3.9 3.1 - - - -
83C PRO* 3.5 23.4 - - - +
127C GLY* 1.3 69.8 - - - -
129C TYR* 1.3 69.5 + - - +
130C THR* 5.6 2.0 - - - +
148C GLU* 4.7 20.2 - - + +
149C PHE 3.9 7.9 - - - +
150C VAL* 4.3 13.2 - - + +
153C VAL* 4.9 0.8 - - + +
155C LEU* 6.5 0.4 - - + -
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Residues in contact with TYR 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 3.8 12.8 - - + -
81C LYS 3.4 4.0 - - - +
82C GLY* 3.6 19.7 - - - -
83C PRO* 3.6 14.9 - - + +
86C ILE* 4.0 6.2 - - + +
88C PHE* 4.1 18.8 - + - -
120C VAL* 4.8 4.5 - - + -
124C MET* 3.4 12.2 - - + +
125C ALA* 2.5 42.8 + - - -
127C GLY 3.5 16.6 - - - -
128C LYS* 1.3 76.0 - - - +
130C THR* 1.3 62.5 + - - +
148C GLU* 3.3 8.3 - - - +
149C PHE* 2.8 74.0 + + + +
151C LYS* 4.0 14.1 - - + -
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Residues in contact with THR 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C SER 3.9 0.5 - - - +
80C ILE* 3.5 3.7 - - - -
81C LYS* 2.7 46.3 + - - +
128C LYS* 5.6 1.7 - - - +
129C TYR* 1.3 75.0 + - - +
131C VAL* 1.3 69.1 + - - +
132C SER* 4.0 3.7 + - - -
146C ASN* 3.8 27.1 - - + +
147C GLN 3.6 7.6 - - - +
148C GLU* 4.5 13.6 + - + +
1272C O4B 3.9 33.0 - - - -
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Residues in contact with VAL 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.7 20.5 - - + +
46C LEU* 4.3 13.2 - - + -
78C LEU* 3.8 17.3 - - + -
79C SER 3.6 3.1 - - - +
80C ILE* 3.6 16.8 - - + -
118C PHE* 3.6 22.7 - - + -
130C THR* 1.3 73.0 - - - +
132C SER* 1.3 62.7 + - - +
146C ASN* 3.2 6.9 - - - +
147C GLN 2.7 39.1 + - - +
149C PHE* 3.3 34.3 - - + -
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Residues in contact with SER 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 3.6 4.7 - - - -
79C SER* 2.8 39.3 + - - -
130C THR* 5.1 4.7 - - - -
131C VAL* 1.3 74.5 - - - +
133C LEU* 1.3 60.9 + - - +
134C GLN* 2.8 40.1 + - - +
144C LYS* 4.3 2.8 - - - +
146C ASN* 3.1 27.8 + - - +
213D ILE* 5.4 5.6 - - - -
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Residues in contact with LEU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 4.2 14.6 - - + -
43C ASN 3.2 29.2 - - - +
44C LEU* 3.8 9.3 - - + +
62C LEU* 4.0 24.7 - - + -
63C GLY 3.9 12.8 - - - +
64C ILE* 4.2 9.9 - - + -
76C TYR* 3.9 23.1 - - + -
77C TRP 3.8 9.9 - - - +
78C LEU* 3.7 13.6 - - + +
132C SER* 1.3 71.9 - - - +
134C GLN* 1.3 69.9 + - - +
135C VAL* 4.6 1.6 - - + -
144C LYS* 3.2 8.0 - - - +
145C ALA* 2.8 39.2 + - + +
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Residues in contact with GLN 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C TYR* 3.2 5.9 - - - +
77C TRP* 3.0 60.2 + - + +
79C SER* 4.9 0.9 - - - -
132C SER* 2.8 39.1 + - - +
133C LEU* 1.3 74.6 - - - +
135C VAL* 1.3 62.5 + - - +
136C VAL 4.3 0.2 - - - -
143C PHE 3.6 3.6 - - - -
144C LYS* 4.0 9.3 - - + +
211D GLY 3.1 23.8 + - - -
212D LEU* 3.2 21.0 - - + +
213D ILE* 2.9 32.7 + - - +
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 4.2 20.9 - - + -
42C ALA* 4.3 14.4 - - + -
64C ILE* 3.9 31.9 - - + -
74C PHE* 3.8 35.7 - - + -
75C LYS 3.5 3.4 - - - +
76C TYR* 4.1 0.9 - - + -
133C LEU* 4.6 4.0 - - + -
134C GLN* 1.3 77.6 - - - +
136C VAL* 1.3 65.5 + - - +
137C ALA 4.5 0.7 - - - +
141C LYS 3.8 1.0 - - - +
142C VAL* 3.5 6.1 - - - +
143C PHE* 2.8 47.9 + - + +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PHE* 3.4 1.7 - - - -
75C LYS* 2.7 42.2 + - + +
77C TRP* 3.6 32.5 - - + -
135C VAL* 1.3 75.3 - - - +
137C ALA* 1.3 63.5 + - - +
138C GLU* 5.0 0.2 - - - -
140C GLY 4.7 2.7 - - - +
141C LYS 3.8 6.7 - - - +
142C VAL* 4.4 4.0 - - + -
212D LEU* 4.0 23.6 - - + -
241D SER* 3.5 40.2 + - - +
242D TYR* 4.1 12.6 - - + -
243D PRO* 4.6 3.8 - - + -
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 5.8 2.0 - - + -
40C ILE* 4.5 9.6 - - + -
72C VAL* 4.7 7.2 - - + -
73C LYS 4.2 4.0 - - - +
74C PHE* 3.8 12.8 - - + +
135C VAL* 4.0 1.6 - - - +
136C VAL* 1.3 76.4 - - - +
138C GLU* 1.3 56.1 + - - +
139C ASN* 3.0 21.3 - - - +
140C GLY* 2.8 26.9 + - - -
141C LYS 3.1 14.5 + - - +
143C PHE* 4.1 14.6 - - + -
241D SER* 3.5 7.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il